D-I-TASSER Q9NPD3

D-I-TASSER results for Q9NPD3

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q9NPD3
Protein Name: Exosome complex component RRP41
Gene Name: EXOSC4

Input Sequence in FASTA format

>Q9NPD3 (245 residues)
MAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRG
SRARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQ
IDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAA
GGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREAS
ILLGD

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q9NPD3-D1	1-245	245		MAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASILLGD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.912

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2po1A	0.93	1.06	0.377	0.963	model1_2po1A.pdb.gz
2	6fszBB	0.93	1.45	0.347	0.988	model1_6fszBB.pdb.gz
3	2ba0F	0.93	1.61	0.369	0.984	model1_2ba0F.pdb.gz
4	2nn6B	0.93	1.11	0.987	0.959	model1_2nn6B.pdb.gz
5	2br2P	0.92	1.42	0.351	0.955	model1_2br2P.pdb.gz
6	2wnrB	0.87	1.18	0.396	0.906	model1_2wnrB.pdb.gz
7	2po1B	0.86	1.91	0.190	0.943	model1_2po1B.pdb.gz
8	3u1kA	0.86	2.44	0.187	0.943	model1_3u1kA.pdb.gz
9	2jeaA	0.86	1.87	0.189	0.931	model1_2jeaA.pdb.gz
10	2wp8B	0.86	1.05	0.361	0.882	model1_2wp8B.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:1901363	0.78	heterocyclic compound binding
GO:0097159	0.78	organic cyclic compound binding
GO:0003824	0.74	catalytic activity
GO:0003676	0.69	nucleic acid binding
GO:0003723	0.66	RNA binding
GO:0016787	0.52	hydrolase activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0071704	0.99	organic substance metabolic process
GO:0044238	0.99	primary metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0016070	0.98	RNA metabolic process
GO:0006401	0.96	RNA catabolic process
GO:0034660	0.93	ncRNA metabolic process
GO:0016072	0.92	rRNA metabolic process
GO:0016075	0.91	rRNA catabolic process
GO:0016071	0.88	mRNA metabolic process
GO:0006396	0.88	RNA processing
GO:0006402	0.87	mRNA catabolic process
GO:0034470	0.86	ncRNA processing
GO:0031123	0.84	RNA 3'-end processing
GO:0006364	0.84	rRNA processing
GO:0000956	0.84	nuclear-transcribed mRNA catabolic process
GO:0031125	0.83	rRNA 3'-end processing
GO:0000291	0.83	nuclear-transcribed mRNA catabolic process, exonucleolytic
GO:0071028	0.82	nuclear mRNA surveillance
GO:0034475	0.82	U4 snRNA 3'-end processing
GO:0034427	0.82	nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'
GO:0071051	0.81	polyadenylation-dependent snoRNA 3'-end processing

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0032991	0.99	macromolecular complex
GO:0044444	0.98	cytoplasmic part
GO:0000178	0.98	exosome (RNase complex)
GO:0044446	0.97	intracellular organelle part
GO:0044428	0.96	nuclear part
GO:0000177	0.96	cytoplasmic exosome (RNase complex)
GO:0043229	0.95	intracellular organelle
GO:0000176	0.95	nuclear exosome (RNase complex)
GO:0005730	0.93	nucleolus

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.398	3b4tA	0.848	1.88	0.246	0.910	2.7.7.56	22,32,42,47,49,128,130,132
2	0.331	1r6lA	0.819	1.48	0.274	0.865	2.7.7.56	47,82,130,133
3	0.328	3dd6A	0.837	2.09	0.226	0.902	2.7.7.56	23,47,130,133
4	0.311	1udoA	0.845	2.02	0.226	0.914	2.7.7.56	47,78,132,134
5	0.060	1rm6A	0.470	5.51	0.047	0.759	1.3.99.20	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.57	2po0A	0.935	1.06	0.377	0.963	1.23	ADP	complex1.pdb.gz	78,83,95,131,132,134,135,178,184,202
2	0.39	3m7nE	0.946	1.37	0.360	0.988	0.90	QNA	complex2.pdb.gz	83,94,95,131,134,135
3	0.31	2c37V	0.920	1.29	0.351	0.955	1.00	U5P	complex3.pdb.gz	78,83,130,132,134,175,178
4	0.27	2c39V	0.915	1.24	0.356	0.947	0.90	ADP	complex4.pdb.gz	99,130,132,133,137,175,178
5	0.21	3h1cC	0.846	2.38	0.207	0.931	1.29	WO4	complex5.pdb.gz	95,99,132,134,178,186
6	0.10	3gmeA	0.830	2.08	0.218	0.898	1.21	III	complex6.pdb.gz	18,20,21,22,24,25,26,27,28,29,30,31,33,219,223,227,230,231

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.